Since Godot has no restrictions on project structure or filesystem usage,
organizing files when learning the engine can seem challenging. This
tutorial suggests a workflow which should be a good starting point.
We will also cover using version control with Godot.

Godot is scene-based in nature, and uses the filesystem as-is,
without metadata or an asset database.

Unlike other engines, many resources are contained within the scene
itself, so the amount of files in the filesystem is considerably lower.

Considering that, the most common approach is to group assets as close
to scenes as possible; when a project grows, it makes it more
maintainable.

As an example, one can usually place into a single folder their basic assets,
such as sprite images, 3D model meshes, materials, and music, etc.
They can then use a separate folder to store built levels that use them.